Contacts of the helix formed by residues 1813 - 1821 (chain C) in PDB entry 5Y3R
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with SER1813 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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393C LYS* 5.0 4.2 - - - -
396C PHE* 4.4 1.5 - - - -
397C LEU* 4.5 16.1 - - - +
433C PRO* 5.2 0.4 - - - +
437C HIS* 3.0 22.6 - - - -
1727C ARG* 3.1 31.2 + - - -
1811C ARG 4.1 0.2 - - - -
1812C LEU* 1.3 69.1 - - - +
1814C PHE* 1.3 56.0 + - - +
1815C THR* 2.9 15.7 + - - -
1816C ARG 4.4 0.9 + - - -
1817C GLN* 4.2 9.2 - - - +
1869C LYS* 4.7 10.6 + - - -
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Residues in contact with PHE1814 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C PHE* 3.2 33.0 - + + -
437C HIS* 3.0 23.1 - - + -
440C VAL* 3.4 31.2 - - + -
441C MET* 3.1 38.6 - - + -
1804C MET* 4.9 11.2 - - + -
1812C LEU 2.7 4.6 + - - +
1813C SER* 1.3 71.4 - - - +
1815C THR* 1.3 55.4 + - - +
1816C ARG 3.3 1.1 - - - -
1817C GLN* 2.9 30.3 + - + -
1818C SER* 2.7 59.0 + - - -
1821C ASP* 5.4 0.2 - - + -
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Residues in contact with THR1815 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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1805C PHE* 4.2 26.9 - - + -
1808C ASP* 5.2 3.8 - - - +
1811C ARG 3.8 12.3 - - - +
1812C LEU* 3.0 23.7 + - + +
1813C SER* 2.9 8.0 + - - -
1814C PHE* 1.3 78.6 - - - +
1816C ARG* 1.3 74.6 + - - +
1818C SER* 3.1 18.6 - - - -
1819C PHE* 4.0 5.2 - - - -
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Residues in contact with ARG1816 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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400C THR* 5.6 0.4 - - - -
1813C SER 4.4 0.8 + - - -
1815C THR* 1.3 88.6 + - - +
1817C GLN* 1.3 59.8 + - - +
1818C SER 2.9 5.6 + - - -
1819C PHE* 3.3 37.6 + - + -
1820C VAL* 3.4 22.3 + - - +
1872C GLY 5.1 8.7 + - - -
1873C TYR* 5.3 7.1 + - - +
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Residues in contact with GLN1817 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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396C PHE* 3.4 26.8 - - + +
397C LEU* 2.8 56.6 + - + +
399C GLN* 3.9 1.4 - - - +
400C THR* 3.0 31.4 + - - +
441C MET* 4.4 3.2 - - + +
1813C SER 4.2 7.3 + - - +
1814C PHE* 2.9 33.6 + - + +
1816C ARG* 1.3 74.5 - - - +
1818C SER* 1.3 66.2 + - - +
1820C VAL* 3.0 18.3 - - - +
1821C ASP* 3.8 3.1 + - - +
1868C THR* 5.8 3.6 - - - +
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Residues in contact with SER1818 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489C ARG* 4.8 14.3 + - - -
1804C MET* 4.7 11.8 - - - +
1814C PHE* 2.7 34.7 + - - -
1815C THR* 3.1 19.3 - - - -
1816C ARG 2.9 1.4 - - - -
1817C GLN* 1.3 73.6 - - - +
1819C PHE* 1.3 65.3 + - - +
1821C ASP* 2.9 30.8 + - - +
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Residues in contact with PHE1819 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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489C ARG* 5.2 12.8 - - - +
1815C THR 4.0 5.8 - - - -
1816C ARG* 3.3 52.7 - - + -
1817C GLN 3.7 0.2 - - - -
1818C SER* 1.3 76.5 - - - +
1820C VAL* 1.3 70.1 + - + +
1821C ASP 3.1 1.6 - - - -
1822C ARG* 2.8 53.8 + - - +
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Residues in contact with VAL1820 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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399C GLN 4.6 4.0 - - - +
400C THR* 3.2 48.2 - - - +
401C ASP 5.1 5.4 - - - +
441C MET* 5.9 1.3 - - + -
1816C ARG 3.4 12.8 - - - +
1817C GLN* 3.0 29.6 - - - +
1819C PHE* 1.3 83.6 - - + +
1821C ASP* 1.3 60.6 + - - +
1822C ARG 2.9 16.5 + - - +
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Residues in contact with ASP1821 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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441C MET* 3.4 20.9 - - + +
445C SER* 2.2 52.9 + - - +
447C PRO* 5.7 0.2 - - - +
490C ILE* 6.1 0.7 - - - +
525C LYS* 3.4 20.3 + - - +
1814C PHE* 5.5 0.2 - - - -
1818C SER 2.9 17.7 + - - +
1820C VAL* 1.3 81.5 - - - +
1822C ARG* 1.3 55.3 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il